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[189868_s_at] choline transporter

Description C48D1.3 /REP_DB=WormBase Gene ID /WP=CE27109 /TR=O02228 /GB=CAB02847.2 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=choline transporter
Cluster 6grp_highest_10_10 > 60      6grp_high1_10_10 > 06      4grp_highest_8_8 > 62      4grp_high_8_8 > 18      6grp_highest_nonorm > 80      6grp_total > 07      4grp_total > 29      6grp_highest_sub > De      6grp_cgc > 11      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 403
1 2 3 4 range
A 430.9
(2.2)
P 		203.2
(-3)
P 		204
(-3)
P 		463.5
(3)
P 		260
B 498
(3)
P 		282.4
(-0.2)
P 		95.4
(-3)
P 		494.8
(3)
P 		403
C 424.5
(3)
P 		397.3
(2.3)
P 		191.6
(-3)
P 		323.6
(0.4)
P 		233
avr 451.1
(3) 		294.3
(-0.3) 		163.7
(-3) 		427.3
(2.5) 		287

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 287
1 2 3 4 5 6 range
A 332.7
(3)
P 		219.3
(-0.4)
P 		145.6
(-2.5)
P 		162
(-2)
P 		150.3
(-2.4)
P 		129.7
(-3)
P 		203
B 258
(3)
P 		245.5
(2.5)
P 		216.3
(1.3)
P 		214.1
(1.2)
P 		132.6
(-2.2)
P 		112.8
(-3)
P 		145
C 399.7
(3)
P 		187.2
(-1.7)
P 		210.7
(-1.2)
P 		128.9
(-3)
P 		142.2
(-2.7)
P 		164.2
(-2.2)
P 		271
avr 330.1
(3) 		217.3
(-0.5) 		190.9
(-1.3) 		168.3
(-2) 		141.7
(-2.8) 		135.6
(-3) 		195
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 137
1 2 3 4 range
A 156.9
(3)
P 		44.1
(-3)
P 		53.3
(-2.5)
P 		67.9
(-1.7)
P 		113
B 158.8
(3)
P 		69.7
(-0.9)
P 		22.1
(-3)
P 		105.4
(0.7)
P 		137
C 140.5
(3)
P 		114.2
(1.2)
P 		66.8
(-2.1)
P 		54.6
(-3)
P 		86
avr 152.1
(3) 		76
(-1.4) 		47.4
(-3) 		76
(-1.4) 		105

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 122
1 2 3 4 5 6 range
A 61.3
(0.8)
P 		78
(3)
P 		31.7
(-3)
P 		41.1
(-1.8)
P 		45.3
(-1.2)
P 		31.6
(-3)
P 		46
B 89.8
(3)
P 		81.7
(2)
P 		52.5
(-1.7)
P 		56.7
(-1.2)
P 		53.9
(-1.5)
P 		42
(-3)
P 		48
C 148.2
(3)
P 		57.1
(-1.5)
P 		53.6
(-1.6)
P 		25.9
(-3)
P 		46
(-2)
P 		55
(-1.6)
P 		122
avr 99.8
(3) 		72.3
(0.2) 		45.9
(-2.5) 		41.2
(-3) 		48.4
(-2.3) 		42.9
(-2.8) 		59
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 189868_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.9154
Sequence Type Exemplar sequence
Representative Public ID C48D1.3 NCBI
Target Description C48D1.3 /REP_DB=WormBase Gene ID /WP=CE27109 /TR=O02228 /GB=CAB02847.2 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=choline transporter
Cluster Evidence This cluster is supported by a Sanger Annotation.
Annotation Method Description
Annotation Description This probe set was annotated using the Matching Probes based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade A annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_070138(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_070138 NCBI Caenorhabditis elegans CHOline transporter family member (cho-1) (cho-1) mRNA, complete cds. 11/11 None
SNAP00000028978 ENSEMBL cdna:SNAP chromosome:CEL140:IV:13209928:13214528:-1 11/11 None
GENEFINDER00000028989 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:13209928:13214528:-1 11/11 None
C48D1.3.1 ENSEMBL cdna:known chromosome:CEL140:IV:13209550:13214535:-1 gene:C48D1.3 11/11 None
C48D1.3.2 ENSEMBL cdna:known chromosome:CEL140:IV:13209697:13214535:-1 gene:C48D1.3 11/11 None
Annotation Notes
There are no noteworthy cross hybridizing mRNAs found for this probe set.
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIV:13209857-13214534(-) 98.05 100.0
Public Domain and Genome References
Gene Title choline transporter
Gene Symbol cho-1
Ensembl C48D1.3
Entrez Gene 178274 Entrez gene
SwissProt O02228 EMBL-EBI
WormBase CE27109 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFAAFFX.4023.1.S1_AT similar to solute carrier family 5 (choline transporter), member 7 cfa
DROSOPHILA_2:1624129_S_AT dm
DROSGENOME1:151892_AT dm
HG-U133_PLUS_2:220722_S_AT solute carrier family 5 (choline transporter), member 7 hs
HG-U133A:220722_S_AT solute carrier family 5 (choline transporter), member 7 hs
HG-FOCUS:220722_S_AT solute carrier family 5 (choline transporter), member 7 hs
HG-U133A_2:220722_S_AT solute carrier family 5 (choline transporter), member 7 hs
HG-U133_PLUS_2:222967_AT solute carrier family 5 (choline transporter), member 7 hs
HG-U133B:222967_AT solute carrier family 5 (choline transporter), member 7 hs
U133_X3P:G11231080_3P_AT solute carrier family 5 (choline transporter), member 7 hs
U133_X3P:G11141884_3P_A_AT solute carrier family 5 (choline transporter), member 7 hs
MOUSE430_2:1421428_AT solute carrier family 5 (choline transporter), member 7 mm
MOE430A:1421428_AT solute carrier family 5 (choline transporter), member 7 mm
MOUSE430A_2:1421428_AT solute carrier family 5 (choline transporter), member 7 mm
RAE230A:1387543_AT solute carrier family 5 (choline transporter), member 7 rn
RAT230_2:1387543_AT solute carrier family 5 (choline transporter), member 7 rn
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6810 transport inferred from electronic annotation QuickGO AmiGO
15871 choline transport inferred from sequence similarity QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
16020 membrane inferred from electronic annotation QuickGO AmiGO
16020 membrane inferred from curator QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
5215 transporter activity inferred from electronic annotation QuickGO AmiGO
15220 choline transporter activity inferred from sequence similarity QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB02847 Hypothetical protein C48D1.3 [Caenorhabditis elegans] ref|NP_502539.1| CHOline transporter family member (cho-1) [Caenorhabditis elegans] sp|O02228|SC5A7_CAEEL High-affinity choline transporter 1 dbj|BAA90483.1| high-affinity choline transporter CHO-1 [Caenorhabditis elegans] 0.0
blast CAE58643 Hypothetical protein CBG01811 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR001734 EMBL-EBI Na+/solute symporter 1.9E-10
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_502539.1 13 4-23,52-71,81-103,132-154,164-186,193-210,235-257,269-291,336-358,379-401,405-427,434-456,471-493
C48D1.3.1 13 4-23,52-71,81-103,132-154,164-186,193-210,235-257,269-291,336-358,379-401,405-427,434-456,471-493
C48D1.3.2 13 4-23,52-71,81-103,132-154,164-186,193-210,235-257,269-291,336-358,379-401,405-427,434-456,471-493
SNAP00000028978 13 4-23,52-71,81-103,132-154,164-186,193-210,235-257,269-291,336-358,379-401,405-427,434-456,471-493
GENEFINDER00000028989 13 4-23,52-71,81-103,132-154,164-186,193-210,235-257,269-291,336-358,379-401,405-427,434-456,471-493
Sequence
Target Sequence 
>C. ELEGANS:189868_S_AT
atgggctttggtatctttgtgcagatttggtctacgtcatactcttccctcaactattat
gtgttgtatatatgccacgtagcaatacgtatggctcattggctggctatgcagtcggtc
ttgtgctccgtttgattggaggcgagccacttgtatcgctgccagcgttcttccattatc
caatgtatacggatggggtacagtatttcccattcaggacaactgctatgttatcttcaa
tggctactatctacattgtatcaatacaatcggagaagctgttcaaatcgggacgtttgt
ctccggagtgggacgtaatgggttgtgtagtgaatattccgatagatcatgtaccccttc
cgtcagatgtatcgtttgc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATGGGCTTTGGTATCTTTGTGCAGA 2 51 1286 Antisense
TACTCTTCCCTCAACTATTATGTGT 680 645 1325 Antisense
ACGTATGGCTCATTGGCTGGCTATG 689 93 1372 Antisense
TGGCTATGCAGTCGGTCTTGTGCTC 404 545 1389 Antisense
TGGAGGCGAGCCACTTGTATCGCTG 94 551 1422 Antisense
TTGTATCGCTGCCAGCGTTCTTCCA 47 709 1436 Antisense
GTATTTCCCATTCAGGACAACTGCT 673 451 1488 Antisense
GTTATCTTCAATGGCTACTATCTAC 336 447 1515 Antisense
CAAATCGGGACGTTTGTCTCCGGAG 631 183 1569 Antisense
ATTCCGATAGATCATGTACCCCTTC 510 7 1621 Antisense
CCCTTCCGTCAGATGTATCGTTTGC 34 257 1640 Antisense
Sequence Source Affymetrix Proprietary Database